Command Agreement
by gawilliams
Summary: An AU presentation of the discussion where Chakotay agrees to become Janeway's First Officer in The Caretaker.
1. Chapter 1

_I never put this one on here at FF, so I am rectifying that mistake. I plan to get back to writing Voyager stories this year, and also finish _A New Mission_ at long last. I do hope those of you who haven't read this particular on before on other sites enjoy it. It was the very first story I wrote almost four years ago. Gregg._

_A/N: This is definitely AU in the sense that I made Chakotay's Starfleet career before he resigned a bit more successful, having been a Captain of two ships before joining the Maquis. It makes for more tension in the discussion and forces Janeway to think hard about what she's doing._

_Disclaimer: I don't own, or profit from, these characters or franchise. No copyright infringement is intended._

The two captains stood appraising one another. One was a short, petite red head who exuded a great deal of confidence and leadership. The other was a tall, dark, and muscular man who sported an interesting tattoo on his forehead above his left eye. One wore the uniform of a Starfleet officer, while the other wore the leathers normally preferred by the Maquis. The question to be resolved was what to do about the dilemma in which they'd found themselves.

For the woman it was a question fraught with entanglements that she would prefer to avoid, but knew that he would not allow her to do so. If she had any hope of coming out of this meeting in command of her own ship, she had to be at her best, and in front of him she was not. For the first time in her life she was deeply attracted to a man with the connection having been instantaneous. Her previous dalliances with love had been wonderful, but had taken time to develop. This was very dangerous territory indeed.

The man was thinking along similar lines. He had felt the immediate pull of her when he first saw her on his view screen and it had been embedded when he had beamed aboard this vessel. His question was, would she follow regulations to the letter once she made the decision to integrate the crews and pass command to him? He outranked her by a few years in grade of captain since he had resigned his commission in that rank and it would be his, along with seniority, once he accepted his commission back. Or would she try to come up with some idea to merge the crews, have him accept his commission, but let her remain in command as the senior officer? It was a dangerous game she would no doubt try to play, but he was inwardly amused as he thought of the ways she would go about it.

"We have a problem, Captain Chakotay," Kathryn Janeway opened with a broad salvo.

"You mean _you_ have a problem, Captain Janeway," he shot back, though he deliberately kept his face cards from view. "From where I stand, I hold all the betting cards."

"Not necessarily," Kathryn replied, showing a little more depth in her move. "There's always the Brig to consider."

He shrugged. "Not likely," he rejoined. "I know your ships status, Captain, and you and I both know you don't have the crew to pull this off. The numbers don't add up. You forget, I've been doing this sort of thing for a while now."

She nodded slightly in recognition of his background in command. Two Starfleet ships of the line and a Maquis vessel. By all accounts he was one of the best commanding officers in the business and rivaled some of the best in history. "I could simply put you in the Brig and press your crew into service." She shifted tactics.

He chuckled. She certainly had moxy. "And you would retain command for perhaps half an hour once you tried that one," he informed her seriously. "Tuvok's good, and your security is top notch, but my crew could take this vessel easily, Captain."

"Then why haven't you?" she angrily threw out. She didn't want to lose her temper, but she also didn't like having her ideas and thoughts so easily shot to pieces. She was also getting angry that she was so turned on by all this. It was not easy being around someone who was actually her equal in this kind of exchange, all rank aside. She had always been the one who excelled against all the competition and no one had ever so easily picked apart her position, personally or professionally.

"I think you know why, Captain," he responded cryptically.

She turned away from him to think about that comment. There was no doubt about what he was referring to, but he was no longer Starfleet. The training, though, was ingrained in officers such as the two of them. The mission above all else, and safety of the crew was at least equal with that. Obviously he wanted them to work together, but he was also not going to be a yes man like her previous First Officer Cavit. That meant if she wanted to retain command, she would have to compromise. _What a mood killer that thought is_, she thought to herself as she turned back to him. Taking a deep breath, she made the one statement she had hoped to avoid.

"What will it take to have you and your crew join Voyager's crew and let me retain my command?" she asked firmly, clearly folding her rapidly losing hand.

Chakotay studied the proud woman in front of him carefully. He'd heard of her over the years, and in fact had almost had her as his First Officer on the last Starfleet ship he'd commanded before resigning two years before, but had chosen a slightly more experienced officer instead. He doubted she even knew how close she'd come to having served as his exec when she was still a commander. In many ways he admired her.

"I'll be your First Officer," he said once his decision was made. He saw the relief clearly showing on her face. He held up his hand. "It comes with a price, though. I won't give up my rank of Captain, though I will, for public consumption wear the field rank bar of a Commander. My crew is to be treated as complete equals with the regular Starfleet crew and be given positions and rank based on skill and experience at the job, not any seniority bullshit."

Kathryn thought about his conditions and they sounded reasonable, though his retention of his rank of Captain, at least between the two of them and according to the ships computer, could be problematic in the case of a dispute between the two of them. "Agreed," she nodded finally. "My condition, though, is that this will be run as a Starfleet vessel and the protocols and regulations will be adhered to."

"I can live with that, so long as you give the Maquis a reasonable chance to learn and not expect immediate acceptance and adherence by people who never went to the Academy," he returned.

"Would three months grace be acceptable on that one?" she asked.

"Make it five," he told her. "It's going to take the first couple to simply place them in the right slots once we find out where everyone best fits."

"Five months," she conceded. "I'll talk to Tuvok and let him know to be lenient about discipline issues. Tom Paris?" she asked.

He scowled darkly, but held back his initial scathing comment. The man had, after all, saved his life. That alone deserved a modicum of respect and a reservation of judgment. "I'm willing to give him a fair chance," he conceded. "I owe him at least that, and I will guarantee his safety among the others of the Maquis who don't hold his best interests at heart."

"Thank you," she responded. "Do you object to him being made the helm officer?"

Chakotay was more than willing to give credit where it was due, even in those whom he personally disliked. "He's the best pilot I've ever seen," he admitted. "We need the best people in the various positions. No objection."

"We can discuss other crew placements when you've had a chance to review the complete picture," Kathryn said finally, when she realized that he had basically finished the overall conversation. She offered her hand to him, though she was inwardly nervous about even shaking his hand considering how aroused the confrontation had made her. Her mind was trying to comprehend it. She was engaged and was not one for casual, lust filled flings. She tried to tamp down the inner voice telling her that her feelings for this man were significantly more than lust.

Chakotay shook her hand and noticed the slight tremor. He smiled inwardly, knowing just how she felt. He knew that she was a much more by the book kind of officer than he had ever been and wondered if he would ever convince her that a rigid reliance on protocol and command distance were not appropriate in Voyager's unique circumstances. He did have a warning to give her, though. Leaning in, he said in a deadly calm voice, "Remember just what my rank really is, Kathryn Janeway," he said powerfully. "Do anything that puts this mission and crew at risk without some incredibly solid reasons and I will re-establish my true rank and assume command as is my right."

Kathryn gulped almost audibly, and shivered. Oh yes, this man was incredibly dangerous, but she knew instinctively that she could trust him and the near constant state of arousal was also nudging her in the direction of trust and something more. It was going to be a very long voyage and she would be taking many cold showers, she had a feeling.

"I know," she said in a near whisper.

She watched as he nodded and stepped out of the Ready Room. Sighing in relief she sank down into her chair and closed her eyes. No matter how she analyzed it, and even though she was still in command, she knew she had lost this round. She would not let that happen again if she could help it.

**Seven Years Later, Kathryn Janeway's Apartment, San Francisco, Earth**

Seven years of cold showers and becoming a near bitch had taken a toll on Kathryn Janeway. Seven years of celibacy were now ending as she slowly sank down on the large erection she had positioned at her entrance. The sting of penetration after so long without was great, but the sheer pleasure of the sex was more than compensatory. She held herself absolutely still as she adjusted to Chakotay's size. Looking down on him she almost cried at the thought of how close she had come to losing him because of her incredible stupidity about protocol. A question lingered, though, and surprisingly she chose now to ask it.

"How come you never assumed your rank and took command out there during all the times I screwed up?" she asked as she clenched her inner muscles. The exquisite feeling of fullness radiated through her, but she was clear headed enough to ask the question.

Chakotay was in a state approaching Nirvana. He was finally in Kathryn Janeway's bed and buried fully within her. He heard her question and stared up at her with wide, bewildered eyes. "You're asking me that now?"

Kathryn smiled and began to slide up and down his length. "I'd say now is the perfect time," she stated calmly, though her breathing was rough and deep. "Or should I just get off of you and let you go back to Seven?"

"NO!" he almost shouted. His ridiculous attempt at a relationship with Seven was something he was not proud of, and he knew that Kathryn wouldn't let him off the hook for a long time to come, though he had to admit her current method of convincing him of where he should be was working pretty damn well. He calmed a bit and moaned as she used her talented muscles to clamp down on him. By the look of complete pleasure on her face he just knew that this had to be her favorite position. He said the only thing he could, and besides which, it was the truth. "Because just like I said to B'Elanna when you destroyed the Caretaker. You're the Captain."

Kathryn continued her slow and languorous ride on top of him, reveling in the feel of it. His statement had a great deal of depth to it and spoke of how much he ultimately trusted her out there. She would tell him later how much it really affected her when she'd heard it, but for now she decided to lean forward and continue his payback.

"And don't you forget it, Captain Chakotay," she said as suddenly a powerful orgasm exploded through her and she was finally able to scream his name at the top of her lungs and give voice to the feelings she had been stifling since that life altering meeting in her Ready Room seven years before.

_A/N: An old one, but one I always enjoyed. Thanks for stopping by and giving it a chance. Gregg._


	2. Chapter 2

_I wrote this years ago as a companion piece to the original Command Agreement which I just posted on this site recently. I am now posting it as the second and concluding chapter to Command Agreement. I hope you enjoy it. Gregg._

_Disclaimer: I don't own, or profit from, these characters or franchise. No copyright infringement is intended._

The rain beat down against the large bay window of Kathryn's apartment as she sipped her coffee and contemplated the last 24 hours. They were home and now she had her dream. Chakotay was laying asleep in her bed in the next room. The sex had been incredible as she always knew it would be, but now she had to deal with the harsh reality that his words to her had shaken loose. "Because you're the Captain," he had said as she slowly rode his impressive erection. The power of those words, said in relation to what she had asked him moments before had almost been her undoing. The enormity of the trust he had so obviously placed in her was now weighing her down and she had to try and deal with it.

The question that was going through her head, and would not leave her, was did she deserve such trust, even though it was now in the past because Voyager was home. A tear fell from her right eye as she briefly thought of the past seven years, particularly the years since New Earth. Professionally she had done what she thought was right, and somehow had got Voyager home. As a person, though, she knew she had failed. After all this time, she now knew that people could be good Captains, but truly great Captains, the ones worthy of emulation and deep respect, were those who allowed their humanity to show the way.

What humanity had she shown? Of course she cared deeply for her crew, but she had hidden it. Command Distance and all that bullshit. More tears fell as she thought of all the times she had used that phrase, as well as the hated word 'protocol'. She'd used them to justify her aloofness and cold, sterile tone when pushing Chakotay away whenever he had crossed one of her ever changing boundaries. Sadly the changes in those boundaries were a narrowing, not an expanding, set.

Naturally he could take only so much and had on rare occasions taken the opportunity during shore leaves to find some female companionship and warm his bed for a few nights. The guilty expression that his eyes reflected on his return from these infrequent leaves told the whole story and she would spend days in personal agony knowing that he was doing something he did not want to do, but to which she had driven him. She had, herself, tried to indulge on one shore leave a couple of years before, but had not been able to go through with it and had asked the young man to leave her room. Even though she had not done anything with the man, she had still felt guilty as hell and had retreated further into her shell.

"Kathryn?"

At the sound of his voice she was startled from her rather negative self-evaluation. The tears were still on her cheeks as she lifted her head to find him kneeling there in front of her. His concern and love clearly shone in his eyes making the tears fall even more. Then she felt him pull her towards him and into his lap as she continued to cry against his shoulder.

Chakotay had woken up to the sounds of quiet sobbing and knew that it had to be Kathryn. Getting up he had found her on the couch with an abandoned coffee cup on the coffee table beside her. Her head was down and she was crying. Kneeling in front of her he'd called her name, the emotions tearing into him as he saw the tears in her eyes, and their wrenching sadness, when she lifted her head. Without hesitation, he'd pulled her into his lap, simply holding her as she cried. He had a fairly good idea what was disturbing her, if her startling question while they were making love was any indication. He also had the sneaking suspicion that she hadn't yet really come to grips emotionally with the overwhelming trauma of being home. She had grown in the years since their first encounter. He had been a real hard ass back then, and had let her know, in no uncertain terms, that he was not going to be a patsy of any kind. She had had to stand her ground since that time, and the confidence gained had made her a better Captain, but her pride and stubborn streak had also held her back from being a truly great Captain. Instead of using that new found confidence positively, she had chosen to sublimate her humanity to an unhealthy, and in many ways dangerous, degree, paying a profound price from her unnecessary, and ultimately foolish, sacrifices.

Kathryn finally settled down and realized that she was in Chakotay's lap and had obviously been crying against his shoulder for some time. The power of her emotions were numbing in their intensity, and she was just now beginning to realize that she had a lot of work to do in order to come to grips with the past seven years. Regardless of the confident lover and woman she had presented to him the night before, she felt a vulnerability that she hadn't felt since that first meeting in her Ready Room all those years ago. At the time she hadn't known if she would still be in command after they were finished. Her innate pride, and stubbornness, had made her resent that instead of recognizing the enormous opportunity he had handed her, and the trust involved in such a sacrifice on his part. He had been the logical one to command, as Tuvok would say, and she had not been willing to look at the gift as anything more than a pushing of her buttons. Her emotional health, and well being, had paid dearly for that terrible mistake on her part.

"Are you okay?" he asked as he stroked her hair for a moment and kissed the top of her head.

"I don't know," she said hesitantly. "I came out here a while ago wanting to savor what we finally have together. Instead I thought of the past and the sort of person I had become out there. Have you ever been disgusted by your own past?"

"Every day," he told her quietly.

She jerked back and looked at him in the eyes. No matter what his words were, his eyes always spoke the truth, though she was one of the few who could read them. She saw a depth of pain and loathing that was shocking. She could also tell that it was directed inward, not at her. "Why?" she asked him. Kathryn knew he hated his Maquis past, though he was proud of the cause they had fought for, but she had never delved into his activities, except to find out from Tuvok that Starfleet's version of events had been wide of the mark and that Chakotay had been one of the truly honorable Maquis, who limited his activities to combating military targets only, and none of them Starfleet.

"Because my actions during the war with Cardassia are ones that I can't ask forgiveness for," he said softly. "I did things that my Father and those who helped raise me would have been viscerally disgusted by and now I have to live with that with no way to offer remorse. For me there is no closure."

Kathryn knew that she had found her closure with their lovemaking the night before, but she also knew that she had a long way to go before she could adequately buffer herself from the self-recriminating thoughts that haunted her. They had each other now, though. Suddenly she knew what had been eluding her. Trust. His overwhelming devotion to her was based on trust, regardless of the circumstances. That was why his statement had hit her so powerfully, and why she was vulnerable now. It was something that needed to be said.

"I think I owe you a profound apology," she told him gently as she took his hand in hers and held it to her heart. "I'm not talking about keeping you at arms length out there, though I know now I was wrong to do so. What I'm apologizing for is for not returning what you gave me. Your trust means so much to me that I don't think words can express how I felt last night when you told me why you never relieved me of command. I never returned that kind of trust, Chakotay, even though you had earned it by the time you forced me to seriously consider B'Elanna for Chief Engineer."

"There are different ways of showing trust, Kathryn," he commented, trying to make her see that it wasn't necessarily a two way street when it came to command. Some latitude needed to be allowed for.

"But you had been a very young, and highly decorated Starfleet Captain," Kathryn rejoined. "That alone should have sent alarm bells clanging when you said you disagreed with me on protocol and the idea of a relationship. Then there was the warning you gave me when you agreed to become First Officer instead of taking command. It was honest, and had the crew at it's center of concern. It scared me, I won't deny, and it got my stubborn streak going in high gear, but you weren't threatening me or my command. You were doing what a damn good exec should do and also what a more experienced Captain should do when everyone is in a real jam like we were. I blinded myself to reality, and I also reacted as if it was all a contest between us. That wasn't worthy of the trust you gave me."

Chakotay continued to listen as she spoke to him about the years on Voyager. She was a very different woman to the one he had originally fallen in love with, but she was a more complete person now. He could see the confidence she had gained, but he was now being allowed to see her vulnerability. The problem was, would she make the same mistakes again if she had it to do over, even knowing what she knew now? He asked her that very question.

"That's what frightens me, Chakotay," she whispered, pulling his hand tighter against her. "A Captain is going to make mistakes, I know that. But I made some hideous ones. The Borg Alliance and the Equinox are two glaring examples, but there were others. We're always taught in Command School that morale is the linchpin of a successful ship and crew. There were times when my actions tore the crew apart and I know that on at least one occasion mutiny was a real possibility. That doesn't even begin to describe the morale issues that were created by how I treated you. Some of the mistakes I could very easily make again, but there are others I wouldn't. I would have a relationship with you, though."

"What's really bothering you, Kathryn?" he asked when he took in her response. "Everything you just said is true, but that was also something that you would have told the Review Board. What was really making you cry?"

Her voice sounded tired and shamed. "I can't forgive myself for pushing you away so much that you found comfort in other women's arms when it got to be too much," she finally admitted. "I tried once, too, but couldn't go through with it."

He was not surprised that she had also sought companionship, but was at her admission of not being able to go through with it. "I was the one in the wrong, Kathryn," he replied.

"No," she said firmly. "I never gave you any hope and you did what you should have after the way I treated your feelings. I refused to look at your beautiful legend as anything more than a professional promise once they came back for us. You may have thought I was angry with you after those shore leaves, but I was really angry with myself and ashamed. I tried avoiding you after them because your guilty look made me feel worse for what I had caused."

"We're together now, though," he pointed out. "And regardless of the past, that's not going to change. The real question is, what are you going to do about it?"

"I was offered a promotion," she told him. "I said I wanted to think about it before letting them know for sure. At the time I was so certain that I'd lost you and the idea of becoming a desk bound officer was my penance. Now that we are together, I think I want to be free. Free from all the rules and nonsense that I foolishly allowed to make such a horrid mess of the last seven years for us. I'd like to retire and just enjoy life with you."

He chuckled. "We certainly can afford to retire, and the book deal that was offered to both of us will certainly set us up for anything," he observed. "Where do you want to live?"

Kathryn snuggled against him even further, enjoying the warm feelings he created within her. Her melancholy was still there, but she was now feeling like she could see ahead of her a genuinely happy life, instead of one that was filled with regret over past mistakes.

"Do you think we could find a secluded area with plenty of forest and a river nearby?" she asked, clearly thinking of their time on New Earth. "We could buy up as much of the land as possible and have it all to ourselves to explore and enjoy. Maybe you could even build us that boat you were designing."

"And perhaps a good sized log cabin to live in?" he suggested.

"And a bathtub big enough for two?" she added with a wide smile. She looked up at him and let him see the love and desire in her eyes. "There will be one major change, though," she added.

"Uh oh," he chuckled.

She playfully slapped his chest. "Listen to me," she told him. "This time I'm giving you my heart, and the blind trust that comes with that. When we made our Command Agreement seven years ago, I didn't give you the trust you deserved, and I belittled you so much afterwards. That won't happen again. This time, we have an equal partnership, and complete trust. I wanted to die inside when I thought I had lost you to Seven. I won't risk that kind of pain again."

"Partners, huh?" he said as he smiled and leaned down to kiss her. "I like the sound of that."

"Really?" she asked with a beaming smile. It hid the butterflies still fluttering in her stomach, but his words were reassuring her a great deal.

"Really," he told her. Then he got serious. "No matter what happens from here on out, Kathryn, equal partners or not, you'll always be the Captain to me. Never doubt that, or the trust that I handed you all those years ago. You earned both."

Before she really broke down, she pulled him in in a tight embrace, then whispered in his ear. "We're both the Captains in this life together, Captain Chakotay," she told him, finally handing him the trust he had shown her. She felt a little bit of life under her bottom which was resting quite comfortably on his lap. Smiling lecherously, she showed a bit of the confidence she had displayed the night before.

"Feels like my new best friend wants to come out and play," she observed with a playful shift of her hips. Then she leaned in and very huskily added, "And I got dibs on top, Mister."

"Aye, Aye, Captain!" Chakotay laughed as he stood with her in his arms. He moved this little party to the bedroom, thinking that he was going to have a very active life with her and it was never going to be dull. He silently thanked Admiral Janeway from the future for making this possible.

_The End._


End file.
